2 external counters on arduino mega

i been thinking of starting a new project which will be using encoders which i would like to count with the external triggered counters. However ive not found any information about setting up 2 on the arduino mega only reference to setting up timer 5. Looking at the schematic and the datasheet it seems i can use Timer/counter 0 and 5 to have 2 external triggered counters. Am i correct? and does anyone have any sample code to test this?

I assume i can use the other timers on board to generate at least 2 pwm outputs and be able to read upto 6 analog inputs as well.

Thank you in advance! :)